| 57 |
|
#include "primitives/Torsion.hpp" |
| 58 |
|
#include "primitives/Inversion.hpp" |
| 59 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
< |
#include "perturbations/ElectricField.hpp" |
| 60 |
> |
#include "perturbations/UniformField.hpp" |
| 61 |
> |
#include "perturbations/UniformGradient.hpp" |
| 62 |
|
#include "parallel/ForceMatrixDecomposition.hpp" |
| 63 |
|
|
| 64 |
|
#include <cstdio> |
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 70 |
|
|
| 71 |
< |
ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL), |
| 72 |
< |
initialized_(false) { |
| 71 |
> |
ForceManager::ForceManager(SimInfo * info) : info_(info), |
| 72 |
> |
initialized_(false), |
| 73 |
> |
switcher_(NULL) { |
| 74 |
|
forceField_ = info_->getForceField(); |
| 75 |
|
interactionMan_ = new InteractionManager(); |
| 76 |
|
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 89 |
|
/** |
| 90 |
|
* setupCutoffs |
| 91 |
|
* |
| 92 |
< |
* Sets the values of cutoffRadius, switchingRadius, cutoffMethod, |
| 91 |
< |
* and cutoffPolicy |
| 92 |
> |
* Sets the values of cutoffRadius, switchingRadius, and cutoffMethod |
| 93 |
|
* |
| 94 |
|
* cutoffRadius : realType |
| 95 |
|
* If the cutoffRadius was explicitly set, use that value. |
| 103 |
|
* SHIFTED_POTENTIAL, or EWALD_FULL) |
| 104 |
|
* If cutoffMethod was explicitly set, use that choice. |
| 105 |
|
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 105 |
– |
* |
| 106 |
– |
* cutoffPolicy : (one of MIX, MAX, TRADITIONAL) |
| 107 |
– |
* If cutoffPolicy was explicitly set, use that choice. |
| 108 |
– |
* If cutoffPolicy was not explicitly set, use TRADITIONAL |
| 106 |
|
* |
| 107 |
|
* switchingRadius : realType |
| 108 |
|
* If the cutoffMethod was set to SWITCHED: |
| 160 |
|
} |
| 161 |
|
} |
| 162 |
|
|
| 163 |
< |
fDecomp_->setUserCutoff(rCut_); |
| 163 |
> |
fDecomp_->setCutoffRadius(rCut_); |
| 164 |
|
interactionMan_->setCutoffRadius(rCut_); |
| 165 |
+ |
rCutSq_ = rCut_ * rCut_; |
| 166 |
|
|
| 167 |
|
map<string, CutoffMethod> stringToCutoffMethod; |
| 168 |
|
stringToCutoffMethod["HARD"] = HARD; |
| 272 |
|
} |
| 273 |
|
} |
| 274 |
|
} |
| 277 |
– |
|
| 278 |
– |
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 279 |
– |
stringToCutoffPolicy["MIX"] = MIX; |
| 280 |
– |
stringToCutoffPolicy["MAX"] = MAX; |
| 281 |
– |
stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL; |
| 282 |
– |
|
| 283 |
– |
string cutPolicy; |
| 284 |
– |
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 285 |
– |
cutPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 286 |
– |
}else if (simParams_->haveCutoffPolicy()) { |
| 287 |
– |
cutPolicy = simParams_->getCutoffPolicy(); |
| 288 |
– |
} |
| 289 |
– |
|
| 290 |
– |
if (!cutPolicy.empty()){ |
| 291 |
– |
toUpper(cutPolicy); |
| 292 |
– |
map<string, CutoffPolicy>::iterator i; |
| 293 |
– |
i = stringToCutoffPolicy.find(cutPolicy); |
| 294 |
– |
|
| 295 |
– |
if (i == stringToCutoffPolicy.end()) { |
| 296 |
– |
sprintf(painCave.errMsg, |
| 297 |
– |
"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n" |
| 298 |
– |
"\tShould be one of: " |
| 299 |
– |
"MIX, MAX, or TRADITIONAL\n", |
| 300 |
– |
cutPolicy.c_str()); |
| 301 |
– |
painCave.isFatal = 1; |
| 302 |
– |
painCave.severity = OPENMD_ERROR; |
| 303 |
– |
simError(); |
| 304 |
– |
} else { |
| 305 |
– |
cutoffPolicy_ = i->second; |
| 306 |
– |
} |
| 307 |
– |
} else { |
| 308 |
– |
sprintf(painCave.errMsg, |
| 309 |
– |
"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n" |
| 310 |
– |
"\tOpenMD will use TRADITIONAL.\n"); |
| 311 |
– |
painCave.isFatal = 0; |
| 312 |
– |
painCave.severity = OPENMD_INFO; |
| 313 |
– |
simError(); |
| 314 |
– |
cutoffPolicy_ = TRADITIONAL; |
| 315 |
– |
} |
| 316 |
– |
|
| 317 |
– |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 275 |
|
|
| 276 |
|
// create the switching function object: |
| 277 |
|
|
| 351 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 352 |
|
} |
| 353 |
|
|
| 397 |
– |
|
| 398 |
– |
|
| 399 |
– |
|
| 354 |
|
void ForceManager::initialize() { |
| 355 |
|
|
| 356 |
|
if (!info_->isTopologyDone()) { |
| 359 |
|
interactionMan_->setSimInfo(info_); |
| 360 |
|
interactionMan_->initialize(); |
| 361 |
|
|
| 362 |
< |
// We want to delay the cutoffs until after the interaction |
| 363 |
< |
// manager has set up the atom-atom interactions so that we can |
| 364 |
< |
// query them for suggested cutoff values |
| 362 |
> |
//! We want to delay the cutoffs until after the interaction |
| 363 |
> |
//! manager has set up the atom-atom interactions so that we can |
| 364 |
> |
//! query them for suggested cutoff values |
| 365 |
|
setupCutoffs(); |
| 366 |
|
|
| 367 |
|
info_->prepareTopology(); |
| 377 |
|
|
| 378 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 379 |
|
|
| 380 |
< |
// Force fields can set options on how to scale van der Waals and |
| 381 |
< |
// electrostatic interactions for atoms connected via bonds, bends |
| 382 |
< |
// and torsions in this case the topological distance between |
| 383 |
< |
// atoms is: |
| 384 |
< |
// 0 = topologically unconnected |
| 385 |
< |
// 1 = bonded together |
| 386 |
< |
// 2 = connected via a bend |
| 387 |
< |
// 3 = connected via a torsion |
| 380 |
> |
//! Force fields can set options on how to scale van der Waals and |
| 381 |
> |
//! electrostatic interactions for atoms connected via bonds, bends |
| 382 |
> |
//! and torsions in this case the topological distance between |
| 383 |
> |
//! atoms is: |
| 384 |
> |
//! 0 = topologically unconnected |
| 385 |
> |
//! 1 = bonded together |
| 386 |
> |
//! 2 = connected via a bend |
| 387 |
> |
//! 3 = connected via a torsion |
| 388 |
|
|
| 389 |
|
vdwScale_.reserve(4); |
| 390 |
|
fill(vdwScale_.begin(), vdwScale_.end(), 0.0); |
| 402 |
|
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 403 |
|
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 404 |
|
|
| 405 |
< |
if (info_->getSimParams()->haveElectricField()) { |
| 406 |
< |
ElectricField* eField = new ElectricField(info_); |
| 405 |
> |
if (info_->getSimParams()->haveUniformField()) { |
| 406 |
> |
UniformField* eField = new UniformField(info_); |
| 407 |
|
perturbations_.push_back(eField); |
| 408 |
|
} |
| 409 |
< |
|
| 409 |
> |
if (info_->getSimParams()->haveUniformGradientStrength() || |
| 410 |
> |
info_->getSimParams()->haveUniformGradientDirection1() || |
| 411 |
> |
info_->getSimParams()->haveUniformGradientDirection2() ) { |
| 412 |
> |
UniformGradient* eGrad = new UniformGradient(info_); |
| 413 |
> |
perturbations_.push_back(eGrad); |
| 414 |
> |
} |
| 415 |
> |
|
| 416 |
|
usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 417 |
|
|
| 418 |
|
fDecomp_->distributeInitialData(); |
| 628 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 629 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 630 |
|
|
| 671 |
– |
|
| 631 |
|
//calculate the center of mass of cutoff group |
| 632 |
|
|
| 633 |
|
SimInfo::MoleculeIterator mi; |
| 634 |
|
Molecule* mol; |
| 635 |
|
Molecule::CutoffGroupIterator ci; |
| 636 |
|
CutoffGroup* cg; |
| 637 |
< |
|
| 638 |
< |
if(info_->getNCutoffGroups() > 0){ |
| 637 |
> |
|
| 638 |
> |
if(info_->getNCutoffGroups() != info_->getNAtoms()){ |
| 639 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 640 |
|
mol = info_->nextMolecule(mi)) { |
| 641 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 659 |
|
RealType electroMult, vdwMult; |
| 660 |
|
RealType vij; |
| 661 |
|
Vector3d fij, fg, f1; |
| 703 |
– |
tuple3<RealType, RealType, RealType> cuts; |
| 704 |
– |
RealType rCut, rCutSq, rListSq; |
| 662 |
|
bool in_switching_region; |
| 663 |
|
RealType sw, dswdr, swderiv; |
| 664 |
|
vector<int> atomListColumn, atomListRow; |
| 676 |
|
Vector3d eField2(0.0); |
| 677 |
|
RealType sPot1(0.0); |
| 678 |
|
RealType sPot2(0.0); |
| 679 |
+ |
bool newAtom1; |
| 680 |
|
|
| 681 |
|
vector<int>::iterator ia, jb; |
| 682 |
|
|
| 683 |
|
int loopStart, loopEnd; |
| 684 |
|
|
| 685 |
< |
idat.rcut = &rCut; |
| 685 |
> |
idat.rcut = &rCut_; |
| 686 |
|
idat.vdwMult = &vdwMult; |
| 687 |
|
idat.electroMult = &electroMult; |
| 688 |
|
idat.pot = &workPot; |
| 699 |
|
idat.f1 = &f1; |
| 700 |
|
idat.sw = &sw; |
| 701 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 702 |
< |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
| 702 |
> |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || |
| 703 |
> |
cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
| 704 |
|
idat.doParticlePot = doParticlePot_; |
| 705 |
|
idat.doElectricField = doElectricField_; |
| 706 |
|
idat.doSitePotential = doSitePotential_; |
| 719 |
|
if (update_nlist) { |
| 720 |
|
if (!usePeriodicBoundaryConditions_) |
| 721 |
|
Mat3x3d bbox = thermo->getBoundingBox(); |
| 722 |
< |
fDecomp_->buildNeighborList(neighborList_); |
| 722 |
> |
fDecomp_->buildNeighborList(neighborList_, point_); |
| 723 |
|
} |
| 724 |
|
} |
| 725 |
|
|
| 726 |
< |
for (vector<pair<int, int> >::iterator it = neighborList_.begin(); |
| 768 |
< |
it != neighborList_.end(); ++it) { |
| 769 |
< |
|
| 770 |
< |
cg1 = (*it).first; |
| 771 |
< |
cg2 = (*it).second; |
| 726 |
> |
for (cg1 = 0; cg1 < point_.size() - 1; cg1++) { |
| 727 |
|
|
| 728 |
< |
fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq); |
| 728 |
> |
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 729 |
> |
newAtom1 = true; |
| 730 |
> |
|
| 731 |
> |
for (int m2 = point_[cg1]; m2 < point_[cg1+1]; m2++) { |
| 732 |
|
|
| 733 |
< |
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 776 |
< |
|
| 777 |
< |
// already wrapped in the getIntergroupVector call: |
| 778 |
< |
// curSnapshot->wrapVector(d_grp); |
| 779 |
< |
rgrpsq = d_grp.lengthSquare(); |
| 780 |
< |
|
| 781 |
< |
if (rgrpsq < rCutSq) { |
| 782 |
< |
if (iLoop == PAIR_LOOP) { |
| 783 |
< |
vij = 0.0; |
| 784 |
< |
fij.zero(); |
| 785 |
< |
eField1.zero(); |
| 786 |
< |
eField2.zero(); |
| 787 |
< |
sPot1 = 0.0; |
| 788 |
< |
sPot2 = 0.0; |
| 789 |
< |
} |
| 733 |
> |
cg2 = neighborList_[m2]; |
| 734 |
|
|
| 735 |
< |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 736 |
< |
rgrp); |
| 737 |
< |
|
| 738 |
< |
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 739 |
< |
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 740 |
< |
|
| 741 |
< |
if (doHeatFlux_) |
| 742 |
< |
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 743 |
< |
|
| 744 |
< |
for (ia = atomListRow.begin(); |
| 745 |
< |
ia != atomListRow.end(); ++ia) { |
| 746 |
< |
atom1 = (*ia); |
| 747 |
< |
|
| 748 |
< |
for (jb = atomListColumn.begin(); |
| 749 |
< |
jb != atomListColumn.end(); ++jb) { |
| 750 |
< |
atom2 = (*jb); |
| 751 |
< |
|
| 752 |
< |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 753 |
< |
|
| 754 |
< |
vpair = 0.0; |
| 755 |
< |
workPot = 0.0; |
| 756 |
< |
exPot = 0.0; |
| 757 |
< |
f1.zero(); |
| 758 |
< |
dVdFQ1 = 0.0; |
| 759 |
< |
dVdFQ2 = 0.0; |
| 760 |
< |
|
| 761 |
< |
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 762 |
< |
|
| 763 |
< |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 764 |
< |
vdwMult = vdwScale_[topoDist]; |
| 765 |
< |
electroMult = electrostaticScale_[topoDist]; |
| 766 |
< |
|
| 767 |
< |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 768 |
< |
idat.d = &d_grp; |
| 769 |
< |
idat.r2 = &rgrpsq; |
| 770 |
< |
if (doHeatFlux_) |
| 771 |
< |
vel2 = gvel2; |
| 772 |
< |
} else { |
| 773 |
< |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 774 |
< |
curSnapshot->wrapVector( d ); |
| 775 |
< |
r2 = d.lengthSquare(); |
| 776 |
< |
idat.d = &d; |
| 777 |
< |
idat.r2 = &r2; |
| 778 |
< |
if (doHeatFlux_) |
| 779 |
< |
vel2 = fDecomp_->getAtomVelocityColumn(atom2); |
| 780 |
< |
} |
| 781 |
< |
|
| 782 |
< |
r = sqrt( *(idat.r2) ); |
| 783 |
< |
idat.rij = &r; |
| 784 |
< |
|
| 785 |
< |
if (iLoop == PREPAIR_LOOP) { |
| 786 |
< |
interactionMan_->doPrePair(idat); |
| 787 |
< |
} else { |
| 788 |
< |
interactionMan_->doPair(idat); |
| 789 |
< |
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 790 |
< |
vij += vpair; |
| 791 |
< |
fij += f1; |
| 792 |
< |
stressTensor -= outProduct( *(idat.d), f1); |
| 793 |
< |
if (doHeatFlux_) |
| 794 |
< |
fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2)); |
| 735 |
> |
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 736 |
> |
|
| 737 |
> |
// already wrapped in the getIntergroupVector call: |
| 738 |
> |
// curSnapshot->wrapVector(d_grp); |
| 739 |
> |
rgrpsq = d_grp.lengthSquare(); |
| 740 |
> |
|
| 741 |
> |
if (rgrpsq < rCutSq_) { |
| 742 |
> |
if (iLoop == PAIR_LOOP) { |
| 743 |
> |
vij = 0.0; |
| 744 |
> |
fij.zero(); |
| 745 |
> |
eField1.zero(); |
| 746 |
> |
eField2.zero(); |
| 747 |
> |
sPot1 = 0.0; |
| 748 |
> |
sPot2 = 0.0; |
| 749 |
> |
} |
| 750 |
> |
|
| 751 |
> |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 752 |
> |
rgrp); |
| 753 |
> |
|
| 754 |
> |
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 755 |
> |
|
| 756 |
> |
if (doHeatFlux_) |
| 757 |
> |
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 758 |
> |
|
| 759 |
> |
for (ia = atomListRow.begin(); |
| 760 |
> |
ia != atomListRow.end(); ++ia) { |
| 761 |
> |
atom1 = (*ia); |
| 762 |
> |
|
| 763 |
> |
for (jb = atomListColumn.begin(); |
| 764 |
> |
jb != atomListColumn.end(); ++jb) { |
| 765 |
> |
atom2 = (*jb); |
| 766 |
> |
|
| 767 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 768 |
> |
|
| 769 |
> |
vpair = 0.0; |
| 770 |
> |
workPot = 0.0; |
| 771 |
> |
exPot = 0.0; |
| 772 |
> |
f1.zero(); |
| 773 |
> |
dVdFQ1 = 0.0; |
| 774 |
> |
dVdFQ2 = 0.0; |
| 775 |
> |
|
| 776 |
> |
fDecomp_->fillInteractionData(idat, atom1, atom2, newAtom1); |
| 777 |
> |
|
| 778 |
> |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 779 |
> |
vdwMult = vdwScale_[topoDist]; |
| 780 |
> |
electroMult = electrostaticScale_[topoDist]; |
| 781 |
> |
|
| 782 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 783 |
> |
idat.d = &d_grp; |
| 784 |
> |
idat.r2 = &rgrpsq; |
| 785 |
> |
if (doHeatFlux_) |
| 786 |
> |
vel2 = gvel2; |
| 787 |
> |
} else { |
| 788 |
> |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 789 |
> |
curSnapshot->wrapVector( d ); |
| 790 |
> |
r2 = d.lengthSquare(); |
| 791 |
> |
idat.d = &d; |
| 792 |
> |
idat.r2 = &r2; |
| 793 |
> |
if (doHeatFlux_) |
| 794 |
> |
vel2 = fDecomp_->getAtomVelocityColumn(atom2); |
| 795 |
> |
} |
| 796 |
> |
|
| 797 |
> |
r = sqrt( *(idat.r2) ); |
| 798 |
> |
idat.rij = &r; |
| 799 |
> |
|
| 800 |
> |
if (iLoop == PREPAIR_LOOP) { |
| 801 |
> |
interactionMan_->doPrePair(idat); |
| 802 |
> |
} else { |
| 803 |
> |
interactionMan_->doPair(idat); |
| 804 |
> |
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 805 |
> |
vij += vpair; |
| 806 |
> |
fij += f1; |
| 807 |
> |
stressTensor -= outProduct( *(idat.d), f1); |
| 808 |
> |
if (doHeatFlux_) |
| 809 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2)); |
| 810 |
> |
} |
| 811 |
|
} |
| 812 |
|
} |
| 813 |
|
} |
| 814 |
< |
} |
| 815 |
< |
|
| 816 |
< |
if (iLoop == PAIR_LOOP) { |
| 817 |
< |
if (in_switching_region) { |
| 818 |
< |
swderiv = vij * dswdr / rgrp; |
| 819 |
< |
fg = swderiv * d_grp; |
| 820 |
< |
fij += fg; |
| 821 |
< |
|
| 822 |
< |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 823 |
< |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 824 |
< |
atomListColumn[0], |
| 865 |
< |
cg1, cg2)) { |
| 814 |
> |
|
| 815 |
> |
if (iLoop == PAIR_LOOP) { |
| 816 |
> |
if (in_switching_region) { |
| 817 |
> |
swderiv = vij * dswdr / rgrp; |
| 818 |
> |
fg = swderiv * d_grp; |
| 819 |
> |
fij += fg; |
| 820 |
> |
|
| 821 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 822 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 823 |
> |
atomListColumn[0], |
| 824 |
> |
cg1, cg2)) { |
| 825 |
|
stressTensor -= outProduct( *(idat.d), fg); |
| 826 |
|
if (doHeatFlux_) |
| 827 |
|
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 828 |
< |
} |
| 829 |
< |
} |
| 830 |
< |
|
| 831 |
< |
for (ia = atomListRow.begin(); |
| 832 |
< |
ia != atomListRow.end(); ++ia) { |
| 833 |
< |
atom1 = (*ia); |
| 834 |
< |
mf = fDecomp_->getMassFactorRow(atom1); |
| 835 |
< |
// fg is the force on atom ia due to cutoff group's |
| 836 |
< |
// presence in switching region |
| 837 |
< |
fg = swderiv * d_grp * mf; |
| 838 |
< |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 839 |
< |
if (atomListRow.size() > 1) { |
| 840 |
< |
if (info_->usesAtomicVirial()) { |
| 841 |
< |
// find the distance between the atom |
| 842 |
< |
// and the center of the cutoff group: |
| 843 |
< |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 844 |
< |
stressTensor -= outProduct(dag, fg); |
| 845 |
< |
if (doHeatFlux_) |
| 846 |
< |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 828 |
> |
} |
| 829 |
> |
} |
| 830 |
> |
|
| 831 |
> |
for (ia = atomListRow.begin(); |
| 832 |
> |
ia != atomListRow.end(); ++ia) { |
| 833 |
> |
atom1 = (*ia); |
| 834 |
> |
mf = fDecomp_->getMassFactorRow(atom1); |
| 835 |
> |
// fg is the force on atom ia due to cutoff group's |
| 836 |
> |
// presence in switching region |
| 837 |
> |
fg = swderiv * d_grp * mf; |
| 838 |
> |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 839 |
> |
if (atomListRow.size() > 1) { |
| 840 |
> |
if (info_->usesAtomicVirial()) { |
| 841 |
> |
// find the distance between the atom |
| 842 |
> |
// and the center of the cutoff group: |
| 843 |
> |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 844 |
> |
stressTensor -= outProduct(dag, fg); |
| 845 |
> |
if (doHeatFlux_) |
| 846 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 847 |
> |
} |
| 848 |
|
} |
| 849 |
|
} |
| 850 |
< |
} |
| 851 |
< |
for (jb = atomListColumn.begin(); |
| 852 |
< |
jb != atomListColumn.end(); ++jb) { |
| 853 |
< |
atom2 = (*jb); |
| 854 |
< |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 855 |
< |
// fg is the force on atom jb due to cutoff group's |
| 856 |
< |
// presence in switching region |
| 857 |
< |
fg = -swderiv * d_grp * mf; |
| 858 |
< |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 859 |
< |
|
| 860 |
< |
if (atomListColumn.size() > 1) { |
| 861 |
< |
if (info_->usesAtomicVirial()) { |
| 862 |
< |
// find the distance between the atom |
| 863 |
< |
// and the center of the cutoff group: |
| 864 |
< |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 865 |
< |
stressTensor -= outProduct(dag, fg); |
| 866 |
< |
if (doHeatFlux_) |
| 867 |
< |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 850 |
> |
for (jb = atomListColumn.begin(); |
| 851 |
> |
jb != atomListColumn.end(); ++jb) { |
| 852 |
> |
atom2 = (*jb); |
| 853 |
> |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 854 |
> |
// fg is the force on atom jb due to cutoff group's |
| 855 |
> |
// presence in switching region |
| 856 |
> |
fg = -swderiv * d_grp * mf; |
| 857 |
> |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 858 |
> |
|
| 859 |
> |
if (atomListColumn.size() > 1) { |
| 860 |
> |
if (info_->usesAtomicVirial()) { |
| 861 |
> |
// find the distance between the atom |
| 862 |
> |
// and the center of the cutoff group: |
| 863 |
> |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 864 |
> |
stressTensor -= outProduct(dag, fg); |
| 865 |
> |
if (doHeatFlux_) |
| 866 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 867 |
> |
} |
| 868 |
|
} |
| 869 |
|
} |
| 870 |
|
} |
| 871 |
+ |
//if (!info_->usesAtomicVirial()) { |
| 872 |
+ |
// stressTensor -= outProduct(d_grp, fij); |
| 873 |
+ |
// if (doHeatFlux_) |
| 874 |
+ |
// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2)); |
| 875 |
+ |
//} |
| 876 |
|
} |
| 912 |
– |
//if (!info_->usesAtomicVirial()) { |
| 913 |
– |
// stressTensor -= outProduct(d_grp, fij); |
| 914 |
– |
// if (doHeatFlux_) |
| 915 |
– |
// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2)); |
| 916 |
– |
//} |
| 877 |
|
} |
| 878 |
|
} |
| 879 |
+ |
newAtom1 = false; |
| 880 |
|
} |
| 881 |
< |
|
| 881 |
> |
|
| 882 |
|
if (iLoop == PREPAIR_LOOP) { |
| 883 |
|
if (info_->requiresPrepair()) { |
| 884 |
< |
|
| 884 |
> |
|
| 885 |
|
fDecomp_->collectIntermediateData(); |
| 886 |
< |
|
| 886 |
> |
|
| 887 |
|
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 888 |
|
fDecomp_->fillSelfData(sdat, atom1); |
| 889 |
|
interactionMan_->doPreForce(sdat); |
| 890 |
|
} |
| 891 |
< |
|
| 891 |
> |
|
| 892 |
|
fDecomp_->distributeIntermediateData(); |
| 893 |
< |
|
| 893 |
> |
|
| 894 |
|
} |
| 895 |
|
} |
| 896 |
|
} |
| 919 |
|
curSnapshot->setLongRangePotential(longRangePotential); |
| 920 |
|
|
| 921 |
|
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 922 |
< |
*(fDecomp_->getExcludedPotential())); |
| 922 |
> |
*(fDecomp_->getExcludedPotential())); |
| 923 |
|
|
| 924 |
|
} |
| 925 |
|
|
| 955 |
|
|
| 956 |
|
if (info_->getSimParams()->getUseLongRangeCorrections()) { |
| 957 |
|
/* |
| 958 |
< |
RealType vol = curSnapshot->getVolume(); |
| 959 |
< |
RealType Elrc(0.0); |
| 960 |
< |
RealType Wlrc(0.0); |
| 958 |
> |
RealType vol = curSnapshot->getVolume(); |
| 959 |
> |
RealType Elrc(0.0); |
| 960 |
> |
RealType Wlrc(0.0); |
| 961 |
|
|
| 962 |
< |
set<AtomType*>::iterator i; |
| 963 |
< |
set<AtomType*>::iterator j; |
| 962 |
> |
set<AtomType*>::iterator i; |
| 963 |
> |
set<AtomType*>::iterator j; |
| 964 |
|
|
| 965 |
< |
RealType n_i, n_j; |
| 966 |
< |
RealType rho_i, rho_j; |
| 967 |
< |
pair<RealType, RealType> LRI; |
| 965 |
> |
RealType n_i, n_j; |
| 966 |
> |
RealType rho_i, rho_j; |
| 967 |
> |
pair<RealType, RealType> LRI; |
| 968 |
|
|
| 969 |
< |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 969 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 970 |
|
n_i = RealType(info_->getGlobalCountOfType(*i)); |
| 971 |
|
rho_i = n_i / vol; |
| 972 |
|
for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) { |
| 973 |
< |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 974 |
< |
rho_j = n_j / vol; |
| 973 |
> |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 974 |
> |
rho_j = n_j / vol; |
| 975 |
|
|
| 976 |
< |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 976 |
> |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 977 |
|
|
| 978 |
< |
Elrc += n_i * rho_j * LRI.first; |
| 979 |
< |
Wlrc -= rho_i * rho_j * LRI.second; |
| 978 |
> |
Elrc += n_i * rho_j * LRI.first; |
| 979 |
> |
Wlrc -= rho_i * rho_j * LRI.second; |
| 980 |
|
} |
| 981 |
< |
} |
| 982 |
< |
Elrc *= 2.0 * NumericConstant::PI; |
| 983 |
< |
Wlrc *= 2.0 * NumericConstant::PI; |
| 981 |
> |
} |
| 982 |
> |
Elrc *= 2.0 * NumericConstant::PI; |
| 983 |
> |
Wlrc *= 2.0 * NumericConstant::PI; |
| 984 |
|
|
| 985 |
< |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 986 |
< |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 987 |
< |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 988 |
< |
curSnapshot->setStressTensor(stressTensor); |
| 985 |
> |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 986 |
> |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 987 |
> |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 988 |
> |
curSnapshot->setStressTensor(stressTensor); |
| 989 |
|
*/ |
| 990 |
|
|
| 991 |
|
} |
